RetrogeneDB ID: retro_hsap_1978

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:20369162..20370224(+)
• Located in intron of: ENSG00000267383

Retrocopy information

• Ensembl ID: ENSG00000213985
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTR2
• Ensembl ID: ENSG00000138071
• Aliases: ACTR2, ARP2
• Description: ARP2 actin-related protein 2 homolog (yeast) [Source:HGNC Symbol;Acc:169]

Sequence

>retro_hsap_1978
ATCAGATCAACCACCAAAGTGGGAAACATTGAAATCAAGGATCTTATGGTTGGTGATGAGGCAAGTGAATTACGATCAAT
GTTAGAAGTTAACTACCCTATGGAAAATGGCATAGTACGAAATTGGGATGACACGAAACACCTGTGGGACTACACATTTG
GACCAGAGAAACCTAATATAGATACCAGAAATTGTAAAATATTACTCACAGAACCTCTTATGAACCCAACCAAAAACAGA
GAGAAGATGGTAGAGGTAATGTTTGAAACTTACCAGTTTTCCGGTGTATATGTAGCCATCCAGGCAGTTCTGACTTTGTA
CGCTCGAGGTTTATTGACTGCTGTAGTGGTAGACTCTGGAGATGGCGTGACTCACATTTACCCAGTATTAGAAGGCTTTT
CTCTCCCTCATCTTACCAGGAGACTGGATATTGCTGGGAGGGATATAACTAGATATCTTATCAAGCTACTTCTGTTGCAA
GGATACACCTTCAACCACTCTGCTGATTTTGAAACGGTTCGCATGATTAAAGAAAAACTGTGTTACGTGGGATATAATAT
TGTGCAAGAGCAGAAACTGGCCTTAGAAACCACAGTATTAGTTGAATCTTATACACTCCCAGATGGAGGAATCATCAAAG
TTGGGGGAGAGAGATTTGAAACACCAGAAGCTTTATTTCAGCCTCACTTGATCAATGTTGAAGGAGTTGGTGTTGCTGAA
TTGCTTTTTAACACAATTCAGGCGGCTGACATTGATACCAGATCTGAATTCTACAAACACATTGTGCTTTCTGGAGGGTC
TACTATGTATCCTGGCCTGTCATCACGGTTGAAACGAGAACTTAAACAGCTTTACTTAGAAAGAGTTTTGAAGGATGATG
CGGAAAAACTTCCTAAATTTAAGATCTGCATTGAAGACCCATCCCGCAGAAAGCACATGGTATTCTTGGGTGGTGCAGTT
CTAGCGGATATCATGAAAGACAAAGACAATTTTTGGATGACCCGACAGGAGTACCAAGAAAAGGGTGTCCTTGTGCTAGA
GAAACTTGGTGTGACTGTTCGA

Alignment

ORF - retro_hsap_1978 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 89.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLT
          IRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDD.KHLWDYTFGPEK.NIDTRNCKILLT
Retrocopy IRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDDTKHLWDYTFGPEKPNIDTRNCKILLT

Parental  EPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
          EP.MNPTKNREK.VEVMFETYQFSGVYVAIQAVLTLYA.GLLT.VVVDSGDGVTHI.PV.EGFSLPHLTR
Retrocopy EPLMNPTKNREKMVEVMFETYQFSGVYVAIQAVLTLYARGLLTAVVVDSGDGVTHIYPVLEGFSLPHLTR

Parental  RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGR
          RLDIAGRDITRYLIKLLLL.GY.FNHSADFETVRMIKEKLCYVGYNI.QEQKLALETTVLVESYTLPDG.
Retrocopy RLDIAGRDITRYLIKLLLLQGYTFNHSADFETVRMIKEKLCYVGYNIVQEQKLALETTVLVESYTLPDGG

Parental  IIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERE
          IIKVGGERFE.PEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGL.SRL.RE
Retrocopy IIKVGGERFETPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLSSRLKRE

Parental  LKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLG
          LKQLYLERVLK.D.EKL.KFKI.IEDP.RRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGV.VLEKLG
Retrocopy LKQLYLERVLKDDAEKLPKFKICIEDPSRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVLVLEKLG

Parental  VTVR
          VTVR
Retrocopy VTVR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.34 RPM	477.01 RPM
bodymap2_adrenal	0.16 RPM	454.89 RPM
bodymap2_brain	0.19 RPM	520.70 RPM
bodymap2_breast	0.23 RPM	339.93 RPM
bodymap2_colon	0.17 RPM	358.78 RPM
bodymap2_heart	0.06 RPM	162.86 RPM
bodymap2_kidney	0.06 RPM	351.17 RPM
bodymap2_liver	0.00 RPM	147.78 RPM
bodymap2_lung	0.00 RPM	364.93 RPM
bodymap2_lymph_node	0.00 RPM	370.68 RPM
bodymap2_ovary	0.10 RPM	316.89 RPM
bodymap2_prostate	0.07 RPM	263.87 RPM
bodymap2_skeletal_muscle	0.05 RPM	143.56 RPM
bodymap2_testis	0.08 RPM	269.54 RPM
bodymap2_thyroid	0.64 RPM	301.71 RPM
bodymap2_white_blood_cells	0.12 RPM	1457.41 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1978 was not detected

EST

No EST(s) were mapped for retro_hsap_1978 retrocopy.

TSS

No TSS is located nearby retro_hsap_1978 retrocopy 5' end.

Lab

retro_hsap_1978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009761	1 retrocopy	retro_btau_707,
Callithrix jacchus	ENSCJAG00000006722	1 retrocopy	retro_cjac_429,
Homo sapiens	ENSG00000138071	1 retrocopy	retro_hsap_1978 ,
Gorilla gorilla	ENSGGOG00000008505	1 retrocopy	retro_ggor_1435,
Monodelphis domestica	ENSMODG00000003364	2 retrocopies	retro_mdom_1082, retro_mdom_754,
Mus musculus	ENSMUSG00000020152	1 retrocopy	retro_mmus_2989,
Pongo abelii	ENSPPYG00000012359	1 retrocopy	retro_pabe_1877,
Pan troglodytes	ENSPTRG00000011990	1 retrocopy	retro_ptro_1320,